NM_001007792.1(NTRK1):c.453del (p.Leu153fs) AND Hereditary insensitivity to pain with anhidrosis

Clinical significance:Pathogenic (Last evaluated: Aug 14, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000807150.2

Allele description [Variation Report for NM_001007792.1(NTRK1):c.453del (p.Leu153fs)]

NM_001007792.1(NTRK1):c.453del (p.Leu153fs)

Gene:
NTRK1:neurotrophic receptor tyrosine kinase 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1q23.1
Genomic location:
Preferred name:
NM_001007792.1(NTRK1):c.453del (p.Leu153fs)
HGVS:
  • NC_000001.11:g.156868218del
  • NG_007493.1:g.57469del
  • NM_001007792.1:c.453del
  • NM_001012331.1:c.543del
  • NM_002529.3:c.543del
  • NP_001007793.1:p.Leu153fs
  • NP_001012331.1:p.Leu183fs
  • NP_002520.2:p.Leu183fs
  • LRG_261t1:c.453del
  • LRG_261t2:c.543del
  • LRG_261t3:c.543del
  • LRG_261:g.57469del
  • LRG_261p1:p.Leu153fs
  • LRG_261p2:p.Leu183fs
  • LRG_261p3:p.Leu183fs
  • NC_000001.10:g.156838010del
  • NM_001012331.1:c.543delG
Protein change:
L153fs
Links:
dbSNP: rs1485714154
NCBI 1000 Genomes Browser:
rs1485714154
Molecular consequence:
  • NM_001007792.1:c.453del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001012331.1:c.543del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_002529.3:c.543del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Hereditary insensitivity to pain with anhidrosis (CIPA)
Synonyms:
FAMILIAL DYSAUTONOMIA, TYPE II; Insensitivity to pain, congenital, with anhidrosis; Neuropathy, congenital sensory, with anhidrosis; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009746; MedGen: C0020074; Orphanet: 642; OMIM: 256800

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000947189Invitaecriteria provided, single submitter
Pathogenic
(Aug 14, 2018)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV001454766Natera, Inc.no assertion criteria providedPathogenic
(Sep 16, 2020)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Novel frameshift and splice site mutations in the neurotrophic tyrosine kinase receptor type 1 gene (NTRK1) associated with hereditary sensory neuropathy type IV.

Verpoorten N, Claeys KG, Deprez L, Jacobs A, Van Gerwen V, Lagae L, Arts WF, De Meirleir L, Keymolen K, Ceuterick-de Groote C, De Jonghe P, Timmerman V, Nelis E.

Neuromuscul Disord. 2006 Jan;16(1):19-25. Epub 2005 Dec 20.

PubMed [citation]
PMID:
16373086

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000947189.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Leu183Trpfs*14) in the NTRK1 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant was reported in the homozygous state in an individual affected with hereditarysensory neuropathy type IV (PMID: 16373086). Loss-of-function variants in NTRK1 are known to be pathogenic (PMID: 10982191). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV001454766.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 23, 2021

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